BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,596,006	A→T	5.2%	intergenic (‑24/+11)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,596,006	0	A	T	5.2%	951.8 / 2.3	336	intergenic (‑24/+11)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base A (151/156); new base T (8/16); total (159/177)
Fisher's exact test for biased strand distribution p-value = 1.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 342 total aligned reads displayed.

AACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAA  >  CP009273/4595941‑4596071

aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCGGACTTTTGTTGatata                                                                 >  1:13180658/1‑67 (MQ=17)

 acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                                >  1:20371876/1‑68 (MQ=255)

 acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                                <  1:17357507/68‑1 (MQ=255)

 acacCTGAAGCTAGCGCGGCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                                <  1:8898091/68‑1 (MQ=255)

  cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                               <  1:22479099/68‑1 (MQ=255)

  cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                               <  1:23185862/68‑1 (MQ=255)

   acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                                >  1:14959543/1‑66 (MQ=255)

   acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCGTACTTTGTTTGATATCGcg                                                              >  1:17669347/1‑67 (MQ=18)

    ccTGAAGGTAGCGCGTCTACGAATTCCGCCACCTTCTCACAGTCATCTTACTTTTTTTGATATCGCCt                                                             <  1:25014866/68‑1 (MQ=25)

    ccTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCt                                                             <  1:13881922/68‑1 (MQ=255)

      tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                           <  1:10444257/68‑1 (MQ=255)

      tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                           <  1:3292100/68‑1 (MQ=255)

      tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                           <  1:14812685/68‑1 (MQ=255)

      tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                           <  1:27344586/68‑1 (MQ=255)

      tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                           <  1:26389731/68‑1 (MQ=255)

       gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                          <  1:11207020/68‑1 (MQ=255)

         aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGttt                                                        >  1:36324505/1‑68 (MQ=255)

         aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGttt                                                        >  1:5003535/1‑68 (MQ=255)

           cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                      >  1:15768798/1‑68 (MQ=255)

            tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                     <  1:38856756/68‑1 (MQ=255)

            tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                     <  1:14589257/68‑1 (MQ=255)

            tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                     <  1:3056545/68‑1 (MQ=255)

            tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                     <  1:36648460/68‑1 (MQ=255)

            tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                     <  1:37444024/68‑1 (MQ=255)

             aGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTg                                                    <  1:32064962/68‑1 (MQ=255)

                 cgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                                <  1:36030345/68‑1 (MQ=255)

                 cgTCTACCAATTCCGCCACCTTCGCACAGTCATATTACTTTATATGATTTCGCCTCGGTTGGGGCGAg                                                >  1:23742122/1‑68 (MQ=21)

                  gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                                <  1:10345671/67‑1 (MQ=255)

                    cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                              <  1:24783705/67‑1 (MQ=255)

                    cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                              <  1:22723694/67‑1 (MQ=255)

                    cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                              <  1:15188215/67‑1 (MQ=255)

                    cTACCAATTCCGCCACCTTCGCACAGTCAACTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                              <  1:39629147/67‑1 (MQ=255)

                        cAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGGATCGGGTTGGGCGAggggggg                                          >  1:11737837/1‑67 (MQ=37)

                         caTTCCGCCACCTTCTAACAGTCATCTAACTTTTTTTGATATCCCCTCTTTTGGTGCGAGGGGGGGGa                                        <  1:4602364/67‑1 (MQ=37)

                         aaTTCCGCCACCTTCCCACAGTCATGTTACTATTTATGATTTCGCCTCCTTTGGTGCGAGGGGGGGGa                                        <  1:34465067/68‑1 (MQ=37)

                          aTTCCGCCACGTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGTGGaa                                       >  1:29083007/1‑67 (MQ=255)

                          aTTCCGCCACCTTCGCAGAGTCATATTACTTTTTTTGATATCGGAGCGTTTGGTGCGAGGCGGGTGaa                                       >  1:18901336/1‑67 (MQ=255)

                          aTTCCGCCACCTTCGCACAGTCATCTTACTTTTTATGATATCGAATCGGGTGGTGGGAgggggggg                                         >  1:19794210/1‑66 (MQ=255)

                            tCCGCCACCTTCGCACAGTCTTCTTACTTTTTTTGATATCGGCTCGGGTGGTGCGAGGGGGGGGACtt                                     >  1:34306910/1‑68 (MQ=38)

                              cGCCACCAACCCACAGTCATCATACTTTTTTTGATATCGCCACGTTTGGTGCGAGGGGGGGGACTTGa                                   <  1:19590953/68‑1 (MQ=25)

                               gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGACTTGaa                                  >  1:33308022/1‑67 (MQ=255)

                                 cACCATCTCACACTCAACATACTTTATTTGATCTCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAAc                                 <  1:5157127/67‑1 (MQ=18)

                                  aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                                >  1:29996386/1‑67 (MQ=255)

                                  aCCTTCGCACAGTCATCTTACTATTATTGATATCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                               <  1:6601523/68‑1 (MQ=37)

                                  aCCTACGCACACGCATCATACTTTTTTTGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                               <  1:17477505/68‑1 (MQ=25)

                                   ccTTCGCGCAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGGAccc                               >  1:26988550/1‑67 (MQ=255)

                                   ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                               >  1:3301557/1‑67 (MQ=255)

                                    cTTCGCACAGTCATCTTACTTTTTTTGAAATCGCCTCGGTTGGTGCGAGGGGTGGGACTTGAcccccc                             >  1:9790312/1‑68 (MQ=37)

                                        tcacaTTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                         <  1:9580188/67‑1 (MQ=255)

                                        tcacaCTCAACTTACATTATTGGATATCCCCTCATTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                         <  1:26858734/67‑1 (MQ=17)

                                        ccacaGGCATCTAACTTTTTTTGATATCGCCACCTTTGGGGCGAGGGGGGGGACTTGAACCCCCACGt                         <  1:37644186/67‑1 (MQ=21)

                                         cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                         >  1:15887767/1‑67 (MQ=255)

                                         cacaGTCATCATACTTTTTTTGATTTACCCAATTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTc                        <  1:25923539/68‑1 (MQ=17)

                                          acaTTCATCTAACATTTTTTGATTTCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       <  1:18170866/68‑1 (MQ=17)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       >  1:38630918/1‑68 (MQ=255)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       >  1:37870798/1‑68 (MQ=255)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       >  1:5759038/1‑68 (MQ=255)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       >  1:30893051/1‑68 (MQ=255)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       >  1:12382835/1‑68 (MQ=255)

                                          acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAACCCCACGTcc                       >  1:33401597/1‑68 (MQ=255)

                                          acaGTCATCTAACTTTTTTTGAAATCGCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                       <  1:14350197/68‑1 (MQ=21)

                                           cattCATCTTACTATTTTTGAAATCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                      <  1:11504460/65‑1 (MQ=18)

                                           caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                      >  1:10001148/1‑68 (MQ=255)

                                           caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                      >  1:17008081/1‑68 (MQ=255)

                                            aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:2805698/1‑68 (MQ=255)

                                            aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:22565638/1‑68 (MQ=255)

                                            aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:13360713/1‑68 (MQ=255)

                                            aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:9361208/1‑68 (MQ=255)

                                             gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                    >  1:20949497/1‑68 (MQ=255)

                                             gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                    >  1:25156138/1‑68 (MQ=255)

                                             gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                    >  1:7927478/1‑68 (MQ=255)

                                             gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACACCAACGTCCGTa                    >  1:2432085/1‑68 (MQ=255)

                                               caacTTACTTTTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                     <  1:6096160/62‑1 (MQ=255)

                                               cATCTTACTTTTTTTGATTTCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                      <  1:12973255/64‑1 (MQ=255)

                                               cATCTTACTTTTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                      <  1:8134986/64‑1 (MQ=255)

                                               cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                    <  1:15469727/66‑1 (MQ=255)

                                                aTCTTACTTTTTTTGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa                 <  1:31426405/68‑1 (MQ=255)

                                                 tCTTACTTTTTTTGAAATCGCCTCGTTTGGTGGGTGGGGGGGGACTTGAACCCCCACGTCCGTAAGaa                <  1:21159613/68‑1 (MQ=21)

                                                  cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCCCGTCCGTAAGAac               >  1:10947956/1‑68 (MQ=255)

                                                   ttACTTTTTTTGAAATCTACAATTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca              <  1:36444028/68‑1 (MQ=14)

                                                   atACATTTATTGAAATCCCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca              <  1:22259373/67‑1 (MQ=17)

                                                    tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:8580372/1‑66 (MQ=255)

                                                    tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:7341375/1‑66 (MQ=255)

                                                    tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:20580415/1‑66 (MQ=255)

                                                    tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:23232180/1‑66 (MQ=255)

                                                    tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGCCCTTCAAACCCCCCGACCGTAAGAacag             >  1:2150521/1‑67 (MQ=25)

                                                    tACCTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:29789983/1‑66 (MQ=255)

                                                    tACATTTTTTGATATACCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac             <  1:31202613/68‑1 (MQ=17)

                                                      cTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGCACACTa           >  1:25507897/1‑68 (MQ=255)

                                                      cTTATTTTGATATCGCCTCGTTTGGAGAGAGGGGTGTTAATTGACCCCCCACGTACGTAAGAACACTa           >  1:35287263/1‑68 (MQ=255)

                                                       tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTaa          >  1:7203941/1‑68 (MQ=255)

                                                       tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTaa          <  1:33806723/68‑1 (MQ=255)

                                                       tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:38274409/1‑67 (MQ=255)

                                                       tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:12474608/1‑67 (MQ=255)

                                                       tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:28725632/1‑67 (MQ=255)

                                                        ttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAac         >  1:18118074/1‑68 (MQ=255)

                                                         tttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAac         >  1:12223838/1‑67 (MQ=255)

                                                         tttttGATATCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:27701533/68‑1 (MQ=255)

                                                         tttttGAATTAGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:6397735/68‑1 (MQ=14)

                                                           tttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        >  1:16825606/1‑66 (MQ=255)

AACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAA  >  CP009273/4595941‑4596071

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`